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==Correlation Spectroscopy Interface==
__TOC___
Corrspecgui is the interactive version of corrspec. The principles of correlation spectroscopy are shown in the demo of corrspec; in the manual in the chapter 'Tutorial for the correlation spectroscopy function corrspec' and for in depth information: W. Windig, D.E. Margevich, W.P. McKenna, A novel tool for two-dimensional (2D) correlation spectroscopy, Chemometrics and Intelligent Laboratory Systems, 28, 1995, 108-128.
==Importing / Exporting==


After starting the program the files are read in through the file menu. The cursor is not displayed until pressing the 'Move cursor to max' button, described below. Often the setting 'Z Origin Equal Zero', described below,is turned on in order to simplify the dispersion matrix.
[[faq_concatenate_multiple_files|How do I concatenate multiple files into a single DataSet?]]


Below the buttons the number of pure variables selected is displayed, followed by editable boxes defining the number of contour levels used in the display of the dispersion matrix and to define the offsets. Below the display of the pure variables the cursor position is displayed.
[[faq_create_multivariate_image_from_separate_images|How do I create a multivariate image from separate images?]]


Below, the buttons and menus of corrspecgui will be discussed. The names of the buttons will be displayed by placing the cursor on top of them.
[[faq_export_PCA_scores_and_loadings_to_text_file|How do I export PCA scores and loadings to a text file (to read into MS Excel, for example)?]]
''Toggle settings display'': turns the settings, displayed on the right, on or off.
''Set pure variable:'' the components defined by the pure variables, indicated by the cross-hair cursor, are eliminated.
''Reset last variable'': undoes the action of the previous 'Set pure variable'.
''Cursor'': enables manual change of cursor position, indicating the pure variables.
''Move cursor to max'': moves the cursor to the maximum in the matrix defined by the setting 'Max Algorithm'.
''Plot At Cursor'': Plots the data at the cursor position in the follow forms:
a) Cursor Variable Plots, a plot of the (pure) variable of the X data set, the (pure) variable of the Y data set, both as a function of axisscale{1} and a plot of both variables, as a visual tool to judge the correlation between these two variables.
b) Cursor Spectrum Plots: a plot of the spectra in the displayed map.
''Inactivate'': Areas that should not be used for pure variables can be inactivated, after which these areas are excluded when the cursor is set to the maximum (by the program of the 'Move cursor to max' button). After clicking one of these buttons the mouse is used to indicate the area to be inactivated. The different inactivate options define whether only the x or y data are inactivated, or both x and y. 
''Reactivate last selection'': Reactivation of the previous inactivated area.
Plot map in 3D: a 3D presentation of the map. Works best with the 'Plot Settings' 'False Color' on. The display can be rotated with the mouse. The button toggles between 3D on and off.
''Resolve spectra'': resolves the data using the pure variables. The resolved results are displayed in the following form:
a)X Spec, X Con, Y spec, Y con, with the resolved spectra and contributions for both X and Y data.
b)X vs Y Con, which shows the resolved X contributions versus the resolved Y contributions, as a tool to judge the correlations between the variables.
c) Maps: the resolved correlation maps.
d) Diagnostics: the original dispersion matrix, the dispersion matrix reconstructed from the resolved components, the sum of the maps shown under the tab 'Maps' and an overlay of these maps, each in a different color.
e) Current plot: clicking on any of the plots mentioned above will display it enlarged under 'Current plot'.


The settings, displayed at the right, have the following functions:
[[faq_import_three-way_data|How do I import three-way data into Solo or PLS_Toolbox?]]
''Load demo data'': loads the data used for the demo in corrspec.
 
''Plot type'': determines plots along the z and y axes of the correlation matrix.
[[faq_import_horiba_NGC_64bit |Why can't I import a Horiba NGC file on my 64-bit computer?]]
''Max Algorithm'': defines the matrix of which its maximum determines pure variables.
 
''Dispersion Algorithm'': defines the matrix displayed.
[[faq_SPCREADR_cant_read_multiple_files |Why can't SPCREADR read multiple files I've selected?]]
''Plot Settings'': determines different aspects of the plots.
 
a) Axis type: defines the continuous or discrete character of plots.
[[faq_some_EXCEL_files_fail_to_import |Why do some Excel files fail to import?]]
b) False color: creates false coloring of the dispersion matrix.
 
c) Z Origin Equal Zero: only displays positive values in dispersion matrix.
==General==
d) Grid: toggle for grid in dispersion matrix.
 
e) Set X/Y direction: plots the x/y axis regular or in reverse.
[[faq_PARALIND_in_PLS_Toolbox |Can I do PARALIND in PLS_Toolbox?]]
f) Color bar: inserts color-bar to indicate z values in plot.
 
g) Colormap: determines which colormap is used.
[[faq_install_on_more_than_one_PC | Can I install PLS_Toolbox (or Solo) on more than one PC, such as on my desktop and laptop computer?]]
 
[[faq_multiple_class_sets_together_in_SIMCA_PLSDA_LDA | Can I use multiple class sets (categorical variables) together in a SIMCA, PLSDA, or LDA model?]]
 
[[faq_more_info_on_R_Squared_statistic | Can you give me more information on the R-Squared statistic?]]
 
[[faq_how_RMSEC_and_RMSECV_related to R2Y_and_Q2Y_seen_other_software | How are RMSEC and RMSECV related to R2Y and Q2Y I see in other software?]]
 
[[faq_convergence_of_PARAFAC| Convergence of PARAFAC. How much variation between models is expected a particular PARAFAC is fit multiple times with the same settings?]]
 
[[faq_does_software_stop_working_if_maintenance_expires | Does the software stop working if my maintenance expires?]]
 
[[faq_report_a_problem_with_PLS_Toolbox | How and where do I report a problem with PLS_Toolbox?]]
 
[[faq_how_are_T_contributions_calculated | How are T-contributions calculated?]]
 
[[faq_how_are_ROC_curves_calculated_for_PLSDA | How are the ROC curves calculated for PLSDA?]]
 
[[faq_how_are_error_bars_calculated_regression_model | How are the error bars calculated for a regression model and can they be related to a confidence limit (confidence in the prediction)?]]
 
[[faq_improve_performance_with_PLS_Toolbx_and_Matlab_on_Mac | How can I improve performance with PLS_Toolbox and Matlab on the Mac platform?]]
 
[[faq_assign_classes_for_samples_in_a_DataSet | How do I assign classes for samples in a DataSet?]]
 
[[faq_build_a_classification_model_from_class_set_other_than_the_first | How do I build a classification model from a class set other than the first?]]
 
[[faq_choose_between_different_cross_validation_leave_out_options | How do I choose between the different cross-validation leave-out options?]]
 
[[faq_reference_Eigenvector| How do I cite/reference Eigenvector?]]
 
[[faq_interpret_ROC_curves_and_Sensitivity_Specificity_plots_from_PLSDA | How do I interpret the ROC curves and Sensitivity / Specificity plots from PLSDA?]]
 
[[faq_make_DataSet_backwards_compatible | How do I make a DataSet backwards compatible?]]
 
[[faq_obtain_or_use_recompilation_license_for_PLS_Toolbox | How do I obtain or use a recompilation license for PLS_Toolbox?]]
 
[[faq_use_custom_cross_validation_option | How do I use the "custom" cross-validation option?]]
 
[[faq_out_of_memory_error_when_analyzing_data | I keep getting "out of memory" errors when analyzing my data. What can I do?]]
 
[[faq_java_lang_OutOfMemoryError| What can I do if I get a java.lang.OutOfMemoryError error?]]
 
[[faq_why_get_negative_scores_when_all_modes_are_set_to_nonnegativity | Nonnegativity (PARAFAC, PARAFAC2, Tucker): Why do I get negative scores when all modes are set to nonnegativity?]]
 
[[faq_what_are_relative_contributions | What are "Relative Contributions"?]]
 
[[faq_what_are_reduced_T^2_and_Q_Statistics | What are the "Reduced" T<sup>2</sup> and Q Statistics?]]
 
[[faq_units_for_RMSEC_and_RMSECV_for_PLSDA | What are the units used for RMSEC and RMSECV when cross-validating PLSDA models?  Why do the cross-validation curves look strange for PLSDA?]]
 
[[faq_what_do_the_four_Fit_/_Unique_Fit_stats_mean_in_MCR_PARAFAC | What do the four Fit/Unique Fit statistics mean in MCR and PARAFAC models?]]
 
[[faq_internal_tests_used_to_select_suggested_number_of_PCs | What internal tests are used to select "suggested" number of PCs?]]
 
[[faq_what_is_PLS1_v_PLS2_and_how_to_create_separate_PLS1_models_from_multi_column_y_block | What is PLS1 vs PLS2 and how do I create separate PLS1 models when I have a multi-column y-block?]]
 
[[faq_difference_between_a_loading_and_a_weighting | What is the difference between a loading and a weighting?]]
 
[[faq_why_some_axis_labels_and_titles_upside_down_in_MIA_Toolbox | Why are some axis labels and titles on my axes upside-down when I'm viewing images in MIA_Toolbox?]]
 
[[faq_why_can't_I_recompile_PLS_Toolbox_functions | Why can't I recompile the PLS_Toolbox functions?]]
 
[[faq_why_get_missing_data_warning| Why do I get the warning/notice "Missing Data Found - Replacing with "best guess" from existing model. Results may be affected by this action."]]
 
[[faq_why_PLS_Toolbox_have_a_boxplot_function_that_conflicts_with_Stats_Toolbox | Why does PLS_Toolbox have a "boxplot" function that conflicts with the Mathworks Statistics Toolbox function of the same name?]]
 
[[faq_why_R2014b_give_error_cannot_convert_double_value_to_a_handle | Why does R2014b give me "Error using matlab.ui.Figure... Cannot convert double value to a handle" (or similar)?]]
 
==Command Line==
[[faq_specify_all_options_of_a_function_or_only_those_different_from_defaults | Do I have to specify all the options to a function or only the ones that are different from the defaults?]]
 
[[faq_how_are_Q_residuals_and_Hotellings_T2_calculated_in_PLS_models | How are the Q-residuals and Hotelling's T<sup>2</sup> values calculated for PLS models?]]
 
[[faq_how_to_automate_PCA_analysis_for_multiple_images  | How do I automate PCA analysis for multiple images?]]
 
[[faq_how_do_I_calculate_my_own_T2_and_Q_limits | How do I calculate my own T<sup>2</sup> and Q limits?]]
 
[[faq_how_do_manually_calculate_the_limits_for_scores | How do I manually calculate the limits for scores?]]
 
[[faq_how_do_I_calculate_scores_from_a_PLS_or_PLSDA_model | How do I calculate scores from a PLS or PLSDA model?]]
 
[[faq_how_do_I_change_the_default_options_for_a_function | How do I change the default options for a function?]]
 
[[faq_how_do_I_interpret_the_misclassification_results_reported_by_crossval | How do I interpret the Misclassification results reported by crossval?]]
 
[[faq_how_do_I_make_PlotGUI_send_plot_to_a_new_figure_and_not_overwrite_current_figure | How do I make PlotGUI send its plot to a new figure and not overwrite the current figure?]]
 
[[faq_how_do_I_retrieve_and_display_predictions_from_a_model_structure_in_command_window | How do I retrieve and display predictions from a model structure in the command window?]]
 
==Manual==
==GUI==
==Installation==
 
 
 
 
 
 
 
[[Category:FAQ]]

Revision as of 13:26, 5 December 2018

_

Importing / Exporting

How do I concatenate multiple files into a single DataSet?

How do I create a multivariate image from separate images?

How do I export PCA scores and loadings to a text file (to read into MS Excel, for example)?

How do I import three-way data into Solo or PLS_Toolbox?

Why can't I import a Horiba NGC file on my 64-bit computer?

Why can't SPCREADR read multiple files I've selected?

Why do some Excel files fail to import?

General

Can I do PARALIND in PLS_Toolbox?

Can I install PLS_Toolbox (or Solo) on more than one PC, such as on my desktop and laptop computer?

Can I use multiple class sets (categorical variables) together in a SIMCA, PLSDA, or LDA model?

Can you give me more information on the R-Squared statistic?

How are RMSEC and RMSECV related to R2Y and Q2Y I see in other software?

Convergence of PARAFAC. How much variation between models is expected a particular PARAFAC is fit multiple times with the same settings?

Does the software stop working if my maintenance expires?

How and where do I report a problem with PLS_Toolbox?

How are T-contributions calculated?

How are the ROC curves calculated for PLSDA?

How are the error bars calculated for a regression model and can they be related to a confidence limit (confidence in the prediction)?

How can I improve performance with PLS_Toolbox and Matlab on the Mac platform?

How do I assign classes for samples in a DataSet?

How do I build a classification model from a class set other than the first?

How do I choose between the different cross-validation leave-out options?

How do I cite/reference Eigenvector?

How do I interpret the ROC curves and Sensitivity / Specificity plots from PLSDA?

How do I make a DataSet backwards compatible?

How do I obtain or use a recompilation license for PLS_Toolbox?

How do I use the "custom" cross-validation option?

I keep getting "out of memory" errors when analyzing my data. What can I do?

What can I do if I get a java.lang.OutOfMemoryError error?

Nonnegativity (PARAFAC, PARAFAC2, Tucker): Why do I get negative scores when all modes are set to nonnegativity?

What are "Relative Contributions"?

What are the "Reduced" T2 and Q Statistics?

What are the units used for RMSEC and RMSECV when cross-validating PLSDA models? Why do the cross-validation curves look strange for PLSDA?

What do the four Fit/Unique Fit statistics mean in MCR and PARAFAC models?

What internal tests are used to select "suggested" number of PCs?

What is PLS1 vs PLS2 and how do I create separate PLS1 models when I have a multi-column y-block?

What is the difference between a loading and a weighting?

Why are some axis labels and titles on my axes upside-down when I'm viewing images in MIA_Toolbox?

Why can't I recompile the PLS_Toolbox functions?

Why do I get the warning/notice "Missing Data Found - Replacing with "best guess" from existing model. Results may be affected by this action."

Why does PLS_Toolbox have a "boxplot" function that conflicts with the Mathworks Statistics Toolbox function of the same name?

Why does R2014b give me "Error using matlab.ui.Figure... Cannot convert double value to a handle" (or similar)?

Command Line

Do I have to specify all the options to a function or only the ones that are different from the defaults?

How are the Q-residuals and Hotelling's T2 values calculated for PLS models?

How do I automate PCA analysis for multiple images?

How do I calculate my own T2 and Q limits?

How do I manually calculate the limits for scores?

How do I calculate scores from a PLS or PLSDA model?

How do I change the default options for a function?

How do I interpret the Misclassification results reported by crossval?

How do I make PlotGUI send its plot to a new figure and not overwrite the current figure?

How do I retrieve and display predictions from a model structure in the command window?

Manual

GUI

Installation